Phylogenetic Inference

While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy (...) prior as a solution of the paradox and argue that it is preferable to a data-size dependent branch lengths prior from a methodological perspective. However, while this reply dissolves the star-tree paradox, the general challenge to Bayesian confirmation theory remains unmet. (shrink)

Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal (...) Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form. (shrink)

There is a certain measure of perplexity concerning the significance of endopolyploidy. It seems that this results from a narrow frame of reference from which investigators view the phenomenon; that is, a predilection for emphasizing the specialized functional aspect of endopolyploidy as it operates in species at the present time overrides any consideration of the rôle that this state may play in the life of a species in its encounter with the forces of natural selection either in the past or (...) in the future.There does not seem to be any obvious relationship between the degree of endopolyploidy that a species can exhibit and either its basic DNA content or the structure of its nucleus. The significance of endopolyploidy may reside not so much in any specialized function that the condition can support, but rather in the properties that are consequent upon the endopolyploid condition itself and which are distinct from those that apply to diploid cells. Some of the properties of the endopolyploid state, and examples of their manifestation in plants and animals, are discussed. The conclusion is that these properties have a potential that opens possibilities for new paths of development and serves as a factor upon which natural selection can operate. (shrink)

Abstract: Under traditional Jewish Law (halacha), assessment of human reproductive cloning (HRC) has been formulated along four lines of inquiry, which I discussed in Part I of this paper. Therein I also analyze five relevant doctrines of Talmudic Law, concluding that under with a risk-benefit analysis HRC fails to fulfill the obligation ‘to be fruitful and multiply’ and should be strictly prohibited. Here, I review of the topic from an exigetical Biblical and Kabbalistic perspective, beginning with exploring comments of the (...) Ramban (Nachmanides) which suggest Kabbalistic insights very much in keeping with current biology. In this Part II of the paper, I expand and annotate statements of the Ramban on the interrelationship of the reproductive faculties of an organism and its soul by examining the development of the spiritual states of plant, animal and human and noting the commensurate evolution with its reproductive facilities. Speculating that the reproductive mechanism of each species is indelibly related to its soul-state, I suggest that interfering with human sexual reproduction by HRC has the same effect the Ramban argues is the result of Kilayim (interbreeding), i.e., wrecking havoc with the Universe. In Part III, I postulate a biologic explanation for warnings found in the Golemic Literature and suggest that these allude to the importance of maintaining human genetic diversity through sexual reproduction. The conclusions I reached after evaluating the propriety of HRC under a Kabbalistic/metaphysical index comports with those I reached using a traditional legal /halachic inquiry in Part I. Thus, both systems arrive at the conclusion that HRC is in violation of the divine and natural order and constitute a distinct biological threat to the survival of the human species, a conclusions in accord with current scientific thinking. (shrink)

© The Author 2017. Published by Oxford University Press on behalf of The Scots Philosophical Association and the University of St Andrews. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com...Richard A. Richards offers a comprehensive introduction to biological classification: ‘the comparison and grouping of organisms, the naming of these groups, the theoretical basis for grouping, and the philosophical foundations for systems of grouping’. This book functions as an introduction to philosophy for biologists, an introduction to biology for philosophers and an (...) introduction to the history of both suitable for a more general audience.In the first chapter, he considers the results of folk and ethno-taxonomy, and related studies in cognitive psychology and developmental linguistics. The results suggest that all humans classify hierarchically, and that there is some agreement between folk and ethno-taxonomy and scientific taxonomy. But, even with this agreement, there is still disagreement about the ‘naturalness’... (shrink)

Here, I consider the recent application of phylogenetic methods in historical linguistics. After a preliminary survey of one such method, i.e. cladistic parsimony, I respond to two common criticisms of cultural phylogenies: that cultural artifacts cannot be modeled as tree-like because of borrowing across lineages, and that the mechanism of cultural change differs radically from that of biological evolution. I argue that while perhaps remains true for certain cultural artifacts, the nature of language may be such as to side-step this (...) objection. Moreover, I explore the possibility that cladistic parsimony can be justified even if is true by appealing to the inference pattern known among philosophers as ‘Inference to the Best Explanation’. (shrink)

Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, because probabilistic assumptions are necessary (...) for calculating the probabilities that define Popper's corroboration, likelihood methods of phylogenetic inference—with their explicit probabilistic basis—are easily reconciled with his concept. In contrast, cladistic parsimony methods, at least as described by certain advocates of those methods, are less easily reconciled with Popper's concept of corroboration. If those methods are interpreted as lacking probabilistic assumptions, then they are incompatible with corroboration. Conversely, if parsimony methods are to be considered compatible with corroboration, then they must be interpreted as carrying implicit probabilistic assumptions. Thus, the non-probabilistic interpretation of cladistic parsimony favored by some advocates of those methods is contradicted by an attempt by the same authors to justify parsimony methods in terms of Popper's concept of corroboration. In addition to being compatible with Popperian corroboration, the likelihood approach to phylogenetic inference permits researchers to test the assumptions of their analytical methods (models) in a way that is consistent with Popper's ideas about the provisional nature of background knowledge. (shrink)

The vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an (...) alternative system are introduced and evaluated. The best aspects of those proposals are brought together to form a post-Linnaean system, and a comparison of the Linnaean and post-Linnaean systems is conducted. The final section of this paper considers not only the theoretical reasons for replacing the Linnaean system, but also the practical feasibility of adopting an alternative system. (shrink)

To cite this Article: Ereshefsky, Marc , 'Foundational Issues Concerning Taxa and Taxon Names', Systematic Biology, 56:2, 295 - 301 To link to this article: DOI: 10.1080/10635150701317401 URL: http://dx.doi.org/10.1080/10635150701317401..

Most biologists use the Linnaean system for constructing classifications of the organic world. The Linnaean system, however, has lost its theoretical basis due to the shift in biology from creationist and essentialist tenets to evolutionary theory. As a result, the Linnaean system is both cumbersome and ontologically vacuous. This paper illustrates the problems facing the Linnaean system, and ends with a brief introduction to an alternative approach to biological classification.

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...) of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations. (shrink)

In a series of articles, Rieppel (2005, Biol. Philos. 20:465–487; 2006a, Cladistics 22:186–197; 2006b, Systematist 26:5–9), Keller et al. (2003, Bot. Rev. 69:93–110), and Nixon and Carpenter (2000, Cladistics 16:298–318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render (...) taxonomy untestable. These charges are unsound. Such charges turn on confusions over rigid designator theory and the distinction between kinds and individuals. In addition, Rieppel’s, Keller et al.’s, and Nixon and Carpenter’s proposed alternatives are no better and have their own problems. The individuality thesis and rigid designator theory should not be quickly abandoned. [Individuals; kinds; PhyloCode; rigid designators; species; taxa; taxon names.]. (shrink)

ABSTRACT ‘Modus Darwin’ is the name given by Elliott Sober to a form of argument that he attributes to Darwin in the Origin of Species, and to subsequent evolutionary biologists who have reasoned in the same way. In short, the argument form goes: similarity, ergo common ancestry. In this article, I review and critique Sober’s analysis of Darwin’s reasoning. I argue that modus Darwin has serious limitations that make the argument form unsuitable for supporting Darwin’s conclusions, and that Darwin did (...) not reason in this way. (shrink)

Among philosophical analyses of Darwin’s Origin, a standard view says the theory presented there had no concrete observational consequences against which it might be checked. I challenge this idea with a new analysis of Darwin’s principal geographical distribution observations and how they connect to his common ancestry hypothesis.

Species serve as both the basic units of macroevolutionary studies and as the basic units of taxonomic classification. In this paper I argue that the taxa identified as species by the Phylogenetic Species Concept (Mishler and Brandon 1987) are the units of biological organization most causally relevant to the evolutionary process but that such units exist at multiple levels within the hierarchy of any phylogenetic lineage. The PSC gives us no way of identifying one of these levels as the privileged (...) level on which taxonomic classifications can be based. (shrink)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...) prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction into a thing . The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs. (shrink)

This chapter explores the idea that phylogenetic diversity plays a unique role in underpinning conservation endeavour. The conservation of biodiversity is suffering from a rapid, unguided proliferation of metrics. Confusion is caused by the wide variety of contexts in which we make use of the idea of biodiversity. Characterisations of biodiversity range from all-variety-at-all-levels down to variety with respect to single variables relevant to very specific conservation contexts. Accepting biodiversity as the sum of a large number of individual measures results (...) in an empirically intractable framework. However, large-scale decisions cannot be based on biodiversity variables inferred from local conservation imperatives because the variables relevant to the many systems being compared would be incommensurate with one another. We therefore need some general conception of biodiversity that would make tractable such large-scale environmental decision-marking. We categorise the large array of strategies for the measurement of biodiversity into four broad groups for consideration as general measures of biodiversity. We compare common moral justifications for the conservation of biodiversity and conclude that some form of instrumental value is the most plausible justification for biodiversity conservation. Although this is often interpreted as a reliance on option value, we opt for a broadly consequentialist characterisation of biodiversity conservation. We conclude that the best justified general measure of biodiversity will be some form of phylogenetic diversity. (shrink)

‘‘Adaptive radiation’’ is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making ‘‘adaptive radiation’’ so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the (...) results of these techniques into categorical ‘‘adaptive radiation: yes/no’’ schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life. (shrink)

Media reporters often announce that we are on the verge of bringing back the woolly mammoth, even while there is growing consensus among scientists that resurrecting the mammoth is unlikely. In fact, current “de-extinction” efforts are not designed to bring back a mammoth, but rather adaptations of the mammoth using close relatives. For example, Harvard scientists are working on creating an Asian elephant with the thick coat of a mammoth by merging mammoth and elephant DNA. But how should such creatures (...) be classified? Are they elephants, mammoths, or both? Answering these questions requires getting clear about the concept of reproduction. What I hope to show is that with an appropriate notion of reproduction—one for which I will argue—resurrecting a member of Mammuthus primigenius is a genuine possibility. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon (...) names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

Early nineteenth century systematists sought to describe what they called the Natural System or the Natural Classification. In the nineteenth century, there was no agreement about the basis of observed patterns of similarity between organisms. What did these systematists think they were doing, when they named taxa, proposed relationships between taxa, and arranged taxa into representational schemes? In this paper I explicate Charles Frederic Girard’s (1822–1895) theory and method of systematics. A student of Louis Agassiz, and subsequently (1850–1858) a collaborator (...) with Spencer Baird, Girard claimed that natural classificatory methods do not presuppose either a special creationist or an evolutionary theory of the natural world. The natural system, in Girard’s view, comprises three distinct ways in which organisms can be related to each other. Girard analyzed these relationships, and justified his classificatory methodology, by appeal to his embryological and physiological work. Girard offers an explicit theoretical answer to the question, what characters are evidence for natural classificatory hypotheses? I show that the challenge of simultaneously depicting the three distinct types of relationship led Girard to add a third dimension to his classificatory diagrams. (shrink)

The term “cladist” has distinct meanings in distinct contexts. Communication between philosophers, historians, and biologists has been hindered by different understandings of the term in various contexts. In this paper I trace historical and conceptual connections between several broadly distinct senses of the term “cladist”. I propose seven specific definitions that capture distinct contemporary uses. This serves to disambiguate some cases where the meaning is unclear, and will help resolve apparent disagreements that in fact result from conflicting understandings of the (...) term. (shrink)

I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...) adequately discussed by proponents of inference to the best explanation. Facing this problem is the price of adopting abductive methods. I sketch an account of how systematists approach the problem of evidence. (shrink)

William Whewell’s work on historical science has received some attention from historians and philosophers of science. Whewell’s own work on the history of German Gothic church architecture has been touched on within the context of the history of architecture. To a large extent these discussions have been conducted separately. I argue that Whewell intended his work on Gothic architecture as an attempt to (help) found a science of historical architecture, as an exemplar of historical science. I proceed by analyzing the (...) key features of Whewell’s philosophy of historical science. I then show how his architectural history exemplifies this philosophy. Finally, I show how Whewell’s philosophy of historical science matches some developments in a science (biological systematics) that, in the mid-to latenineteenth century, came to be reinterpreted as a historical science. I comment briefly on Whewell as a potential influence on nineteenth century biology and in particular on Darwin. (shrink)

Ontological questions in biology have typically focused on the nature of species: what are species; how are they identified and individuated? There is an analogous, but much neglected concern: what are characters; how are they identified and individuated? Character individuation is significant because biological systematics relies on a parsimony principle to determine phylogeny and classify taxa, and the parsimony principle is usually interpreted to favor the phylogenetic hypothesis that requires the fewest changes in characters. But no character individuation principle identified (...) so far is adequate. For biological systematics we need a better way of conceiving characters. (shrink)

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be (...) recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept. (shrink)

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

If asked to explain why the Golds’ treatment of other colors in Red Rising is wrong, it is tempting to say something like “they are all human beings, and it is wrong to treat humans in this way!” In this essay, I’ll argue that this simple answer is considerably complicated by the fact that the different colors might not be members of the same biological species, and it is in fact unclear whether any of them are the same species as (...) current humans. Explaining why exactly this is so will lead us to an exploration the long-running debate in biology and philosophy over what exactly it means for two organisms to be “members of the same species.” I’ll begin by discussing the biological essentialism of Aristotle and his followers, who held that an individual organism’s species was determined by essence. One can easily imagine that the Golds might find this attractive, since it would suggest that their “superior” mental and physical capacities made them a different (and probably “higher”) species of humanity than the other colors. Unfortunately for Aristotle, this turns out to be inconsistent with Charles Darwin’s account of evolution by natural selection. This development has led many modern biologists and philosophers of biology to conceptualize species not as an abstract “form” that serves to classify organisms, but rather as a concrete collection of organisms relatively close to each other in space and time. In contrast to biological essentialism, this view of “species as concrete individual” might seem to support the Reds’ claim to the “same species” as the Gold, since they are both part of the same overarching society. Next, I’ll consider how we might tell where one species “ends” and another one “begins.” As it turns out, biologists have many ways of answering his question, each of which makes different judgments about the species of Red Rising’s characters. So, for example, the “Biological Species Concept” bases judgements about species membership on the ability to produce fertile offspring. This concept is far from perfect, however, for reasons that Red Rising makes clear: it doesn’t deal clearly with cases where reproduction is possible but very difficult (a Red and a Gold having a child) or for organisms that do not reproduce sexually (such as Pinks). I’ll then explore a few prominent alternatives to BSC, including both genetically and ecologically based species concepts, and consider their consequences for the society of Red Rising. I’ll conclude by advocating for a “pluralism” about species membership, and will suggest that the people of Red Rising (as well as in the real world) should beware of basing arguments for moral or political equality on the all-too-slippery notion of “shared humanity.” Instead, they should focus on the qualities that make the lives of the individuals (regardless of their species) worth caring about, such as their shared desires to avoid suffering and to lead fulfilling, meaningful lives. (shrink)

Common ancestry is one of the pillars of Darwin’s theory of evolution. Today, the Tree of Life, which represents how all life is genealogically related, is often thought of as an essential component in the foundations of biological systematics and so therefore of evolutionary theory – and perhaps all of biology itself. It is an iconic representation in biology and even penetrates into popular culture.

The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...) is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species. (shrink)

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods (...) of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally. (shrink)

A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge networks by (...) fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. (shrink)

Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...) Sergey Gavrilets on adaptive landscapes, using migration rate, or gene flow, as the primary scale, and concluding that adaptive and drift explanations are complementary rather than competing. I propose a distinction between intrinsic and extrinsic selection, and the notion of reproductive reach and argue that speciation modes should be discriminated in terms of gene flow, the nature of selection maintaining reproductive reach, and whether the predominant cause is selective or stochastic. I also suggest that the notion of an adaptive “quasispecies” for asexual species is the primitive notion of species, and that members of reproductively coherent sexual species are additionally coadapted to their mating partners. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

The cladistic species concept proposed by Ridley (1989) rests on an undefined notion of speciation and its meaning is thus indeterminate. If the cladistic concept is made determinate through the definition of speciation, then it reduces to a form of whatever species concept is implicit in the definition of speciation and fails to be a truly alternative species concept. The cladistic formalism advocated by Ridley is designed to ensure that species are monophyletic, that they are objectively real entities, and that (...) they are individuals. It is argued that species need not be monophyletic in order to be real entities, and that ancestor-descendant relations are not the only relations that confer individuality on entities. The species problem is recast in terms of a futile quest for a definition of that single kind of entity to which the term species should uniquely apply. (shrink)